|
| Status |
Public on Jul 24, 2014 |
| Title |
OPGP Sample 400899NK |
| Sample type |
genomic |
| |
|
| Source name |
lymphoblastoid cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: lymphoblastoid cell line
gender: female
ethnicity: European
|
| Treatment protocol |
None
|
| Growth protocol |
Cell lines were grown according to standard conditions.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lymphocyte isolation by the Ficoll separation procedure followed by cryopreservation and storage in liquid nitrogen. Cell lines were established using EBV-transformation.
|
| Label |
biotin
|
| Label protocol |
DNA was restriction digested, PCR amplified, fragmented, and labeled as per the manufacturer (Affymetrix).
|
| |
|
| Hybridization protocol |
DNA was hybridized to the array at 50C for 17 hours according to the manufacturer's instructions. The arrays were washed using Affymetrix Fluidics Stations.
|
| Scan protocol |
The arrays were scanned using the GeneChip Scanner 3000.
|
| Description |
Sample name: 400899NK
|
| Data processing |
CYCHP files generated by Chromosome Analysis Suite (ChAS) version 1.15.0 (Affymetrix Linux apt program) are provided:
affymetrix-algorithm-name = CYTO2
affymetrix-algorithm-version = 1.15.0
program-name = apt-copynumber-cyto
program-version = 1.15.0
affymetrix-algorithm-param-option-reference-input = opgp953.REF_MODEL
To achieve comprehensive CNV calling, we used four separate algorithms to detect CNVs: Affymetrix Chromosome Analysis Suite (ChAS), iPattern, Nexus and Partek. Our primary analysis was performed based on ChAS CNV calls, which were then supported using the remaining three algorithms to construct a confidence set of CNVs14. For all algorithms, we have used 8 probes and >1kb as a base line cutoff for CNV detection.
|
| |
|
| Submission date |
Jul 23, 2014 |
| Last update date |
Jul 24, 2014 |
| Contact name |
Stephen W Scherer |
| E-mail(s) |
[email protected]
|
| Organization name |
The Hospital for Sick Children
|
| Department |
Genetics and Genomic Biology
|
| Street address |
686 Bay Street
|
| City |
Toronto |
| State/province |
Ontario |
| ZIP/Postal code |
M5G 0A4 |
| Country |
Canada |
| |
|
| Platform ID |
GPL16131 |
| Series (1) |
| GSE59150 |
A High-Resolution Copy Number Variation Resource for Clinical Genetics |
|
